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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCCAAAAGCACTCACTGAGAAAGAACAACAAGAGCTTGTTGATCTCGTCGATGTCAAGCTTGGTCAGGAGTACGAGCTTGTTGTCACCACCTATGCTGgtaagaaaaccaaccacctttcattgatttgctttggttaccaaaagattgaatctttccaactaaaagtgagaatcttcaattcatttgtttacaaaagattgaatgttgtgttgttttgtgattttctatgcag

Basic information

species Arabidopsis thaliana
transcript AT5G54510.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G54510.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G366873_T02 (Zea mays), 5'ss of exon 1
-CTTCCAAAAGCACTCACTGAGAAAGAACAACAAGAGCTTGTTGATCTCGTCGATGTCAAGCTTGGTCAGGAGTACGAGCTTGTTGTCACCACCTATGCTGgtaagaaaaccaaccacctttcattgatttgct-ttggttaccaaaagattgaatctttccaactaaaagtgagaatcttcaattcatttgtttacaaaagattgaatgttgtgttgttttgtgattttctatgcag
     ||    |   | | ||    || || |  || || || || |||||||| |||||||| || || ||||||||||| || |||||||||||  | |||  |    |     |  |   || ||   |||  | | |    |   | |||  ||  | | |||    | |  | | |  |  ||        |     | || |                              
GGCGGCACCGACGA-CGCCGATCCCGACCATCGCGACCTCGTGGACCTCGTCGACGTCAAGCTCGGGCACGAGTACGAGCTCGTCGTCACCACCTACTCAGgtgcgggtgcgggtga--tgaaatggaacagctgctagctgatgagtcagtgacactagctagctagc--taacgaacgtacacgcacgcacgc-cgtgcaactgcag-----------------------------

upper sequence: AT5G54510.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA12G17510.1 (Glycine max), 5'ss of exon 2
CTTCCAAAAGCACTCACTGAGAAAGAACAACAAGAGCTTGTTGATCTCGTCGATGTCAAGCTTGGTCAGGAGTACGAGCTTGTTGTCACCACCTATGCTGgtaagaa-aaccaaccacctttcattgat-ttgctttggttaccaaaagattgaatctttccaactaaaagtgagaatcttcaattcatttgtttacaaaagattgaatgttgtgttgttttgtgattttctatgcag
   || | | | |||| |||||| ||||| || ||||| ||||| || || |||||||| ||||| || || || || ||||||||||| || ||||||||| |||| || |||  ||      ||| | |||      ||| |  || |||     | |     |  || |     ||     ||  |||  |||| |    |                                  
ACCCCCAGATCCCTCAATGAGAAGGAACAGCAGGAGCTGGTTGAGCTTGTTGATGTCAAACTTGGCCAAGAATATGAACTTGTTGTCACAACTTATGCTGgtgagaataatcaaaaacacccttttgttattgtcacatttatcttaacatta----tctaaggttttaaattgcggtcgcggttttgtttcattaccatcctt----------------------------------

upper sequence: AT5G54510.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv19s0014g04690.t01 (Vitis vinifera), 5'ss of exon 2
CTTCCAAAAGCACTCACTGAGAAAGAACAACAAGAGCTTGTTGATCTCGTCGATGTCAAGCTTGGTCAGGAGTACGAGCTTGTTGTCACCACCTATGCTGgtaagaaaaccaaccacctttcattgatttgctttggttaccaaaagattgaatctttccaactaaaagtgagaatcttcaattcatttgtttacaaaagattgaatgttgtgttgttttgtgattttctatgcag
 | || ||| | |||| ||| || || ||||||||  | || ||||||||||||||||||||||| |||||||| ||||| || |||||||| ||||| ||| ||    || ||    ||   || ||||  ||   ||  |     | || ||  |   |  || | || |  | |||  || |    |                                              
GTCCCCAAATCCCTCAATGACAAGGAGCAACAAGACTTGGTCGATCTCGTCGATGTCAAGCTTGGGCAGGAGTATGAGCTGGTCGTCACCACTTATGCCGgtcagttgcccgacataattgacttaatttttttcatttgtctttcaaatgtatgctgata--tatatgtcatgaactt-gatgctgcag----------------------------------------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|116465722|gb|EG508314.1|EG508314
EST:     CGATGTCAAGCTTGGTCAGGAGTACGAGCTTGTTGTCACCACCTATGCTG                         GGCTTTACAGGTACAGAGTGGGTGATGTCCTAAGCGTGGCTGGTTTCAAGA
genomic: CGATGTCAAGCTTGGTCAGGAGTACGAGCTTGTTGTCACCACCTATGCTGgtaagaaaac ... ttctatgcagGGCTTTACAGGTACAGAGTGGGTGATGTCCTAAGCGTGGCTGGTTTCAAGA
EST: gi|124958929|gb|EL033639.1|EL033639
EST:     CGATGTCAAGCTTGGTCAGGAGTACGAGCTTGTTGTCACCACCTATGCTG                         GGCTTTACAGGTACAGAGTGGGTGA
genomic: CGATGTCAAGCTTGGTCAGGAGTACGAGCTTGTTGTCACCACCTATGCTGgtaagaaaac ... ttctatgcagGGCTTTACAGGTACAGAGTGGGTGA
EST: gi|116483570|gb|EG526162.1|EG526162
EST:     CGATGTCAAGCTTGGTCAGGAGTACGAGCTTGTTGTCACCACCTATGCTG                         GGCTTTACAGGTACAGAGTGGGTGATGTCCTAAGCGTGGCTGGTTTCAAGA
genomic: CGATGTCAAGCTTGGTCAGGAGTACGAGCTTGTTGTCACCACCTATGCTGgtaagaaaac ... ttctatgcagGGCTTTACAGGTACAGAGTGGGTGATGTCCTAAGCGTGGCTGGTTTCAAGA
EST: gi|124970052|gb|EL043909.1|EL043909
EST:     CGATGTCAAGCTTGGTCAGGAGTACGAGCTTGTTGTCACCACCTATGCTG                         GGCTTTACAGGTACAGAGTGG
genomic: CGATGTCAAGCTTGGTCAGGAGTACGAGCTTGTTGTCACCACCTATGCTGgtaagaaaac ... ttctatgcagGGCTTTACAGGTACAGAGTGG
EST: gi|116482415|gb|EG525007.1|EG525007
EST:     CGATGTCAAGCTTGGTCAGGAGTACGAGCTTGTTGTCACCACCTATGCTG                         GGCTTTACAGGTACAGAGTGGGTGATGTCCTAAGCGTGGCTGGTTTCAAGA
genomic: CGATGTCAAGCTTGGTCAGGAGTACGAGCTTGTTGTCACCACCTATGCTGgtaagaaaac ... ttctatgcagGGCTTTACAGGTACAGAGTGGGTGATGTCCTAAGCGTGGCTGGTTTCAAGA
EST: gi|116465777|gb|EG508369.1|EG508369
EST:     CGATGTCAAGCTTGGTCAGGAGTACGAGCTTGTTGTCACCACCTATGCTG                         GGCTTTACAGGTACAGAGTGGGTGATGTCCTAAGCGTGGCTGGTTTCAAGA
genomic: CGATGTCAAGCTTGGTCAGGAGTACGAGCTTGTTGTCACCACCTATGCTGgtaagaaaac ... ttctatgcagGGCTTTACAGGTACAGAGTGGGTGATGTCCTAAGCGTGGCTGGTTTCAAGA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCCAAAAGCACTCACTGAGAAAGAACAACAAGAGCTTGTTGATCTCGTCGATGTCAAGCTTGGTCAGGAGTACGAGCTTGTTGTCACCACCTATGCTGgtaagaaaaccaaccacctttcattgatttgctttggttaccaaaagattgaatctttccaactaaaagtgagaatcttcaattcatttgtttacaaaagattgaatgttgtgttgttttgtgattttctatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG